Metastable austenitic stainless steels are materials that can undergo austenite to martensite phase transformation when subjected to deformation and thus they represent a multiphase material with interesting mechanical properties. Different electron microscopy techniques are widely applied for the characterization of their deformation mechanisms at micrometric length scale. In doing so, Scanning Ion Microscopy (SIM) imaging, performed with a Focused Ion Beam (FIB), can be useful to evaluate microstructural features induced by different stress fields and, in certain cases, may substitute the conventional Transmission Electron Microscopy (TEM) technique. In this work, nanoindentation experiments (both monotonic and cyclic) were carried out on AISI 301LN metastable steel in order to induce localized deformation of individual austenitic grains. The activated plastic deformation mechanisms were evaluated by using different advanced characterization techniques (Electron BackScattered Diffraction (EBSD) and TEM), but mainly by FIB/SIM. FIB/SIM 3D-tomography was also conducted to reconstruct the deformation structure under the residual imprint. These observations, surprisingly, showed the existence of a good correlation between SIM and TEM images, concerning phase transformation and plastic zone development.